Amino Acids and Proteins

Question 1

What is meant by all amino acids are amphoteric?

Answer 1

They have the ability to act as acids and bases in reactions.

Question 2

pKa of carboxyl and amino groups

Answer 2

carboxyl = 2

amino groups = 10

Question 3

When the pH of the solution is less than the pKa of an acidic group, the acidic group will be mostly__

Answer 3

When the pH of the solution is less than the pKa of an acidic group, the acidic group will be mostly in its protonated form

Question 4

When the pH of the solution is greater than the pKa of an acidic group, the acidic group will be mostly____

Answer 4

When the pH of the solution is greater than the pKa of an acidic group, the acidic group will be mostly in its deprotonated form

Question 5

henderson hasselbalch equation

Question 6

calculating pI of a molcule (i.e. AA) with 2 functional groups

Answer 6

average the pKa’s of the two functional groups

Question 7

How to compare the pH of a solution to the pKa of the functional group of an AA and determine if a site is mostly protonated or deprotonated?

Answer 7

If the pH is higher than the pKa, the site is mostly deprotonated; if the pH is lower than the pKa, the site is mostly protonated

Question 8

How are polypeptides linked together

Answer 8

Peptide bond - b/w the carboxyl group of one AA and the α-amino group of the another AA

Question 9

polypeptide backbone formation

Answer 9

N-C-C-N-C-C

Question 10

How do we break apart proteins?

Answer 10

Via Hydrolysis, by another protein called a proteolysis or proteolytic cleavage and the enzyme is called a protease

Question 11

Primary protein structure

Answer 11

AA sequence

Question 12

Secondary structure

Answer 12

H-bonding between the backbone groups (NH and CO)

Question 13

Tertiary Structure

Answer 13

folding due to side chain interactions within a polypeptide

Question 14

types of interactions in Tertiary Structure

Answer 14

Noncovalent

1. acid/base (electrostatic)
2. polar/polar
3. nonpolar/nonpolar

Covalent

1. disulfide bridges (b/w cysteine)

Question 15

Quaternary Structure

Answer 15

side-chain inreractions between different polypeptides.

NOT all proteins have this structure

Question 16

How do we drive endergonic reactions forward?

Answer 16

couple it with exergonic reactions

Question 17

Hydrolase

Answer 17

hydrolyzes chemical bonds (including ATPases, proteases, and others)

Question 18

Isomerase

Answer 18

rearranges bonds within a molcule to form an isomer (i.e. second half of PPP)

Question 19

Ligase

Answer 19

forms a chemical bond (e.g., DNA ligase)

Question 20

Lyase

Answer 20

breaks chemical bonds by means other than oxidation or hydrolysis (e.g., pyruvate decarboxylase)

Question 21

Kinase

Answer 21

transfers a phosphate group to a molcule from a high energy carrier, such as ATP (e.g., phosphofructokinase [PFK])

Question 22

Oxioreductase (give examples as well)

Answer 22

runs redox reactions (includes oxidaes, reductases, dehydrogenases, and others)

Question 23

Polymerase

Answer 23

polymerization (e.g. addition of nucleotides to the leading strong of DNA by DNA polymerase III)

Question 24

Phosphatase

Answer 24

removes a phosphate group from a molecule

Question 25

Phosphorylase

Answer 25

transphers a phosphate group to a molecule from inorganic phosphate (e.g., glycogen phosphorylase)

Question 26

Protease

Answer 26

hydrolizes peptide bonds (e.g., trypsin, chymotrypsin, pepsin, etc.)

Question 27

Cofactors

Answer 27

metal ions or small molecules (not themselves a protein) that are required for activity in many enzymes. Vitamins in our diet serve as precursors for cofactors

Question 28

coenzymes

Answer 28

when a cofactor is an organic molecule

Question 29

What is K_m?

Answer 29

K_m is the concentration of substrate [S] required to reach 1/2 V_max

Question 30

explain affinity and Km

Answer 30

It is like an affinity the enzyme has for the substrate and has an inverse relationship. Increase affinity = decreased Km (less substrate needed to reach Km)

Question 31

What is meant by Vmax what does it depend on?

Answer 31

Vmax is the maximum rate of product formation, when the enzymes are completely saturated by substrate * Depends on:* - enzymes you have - enzyme concentration - NOT impacted by substrate

Question 32

Competitive Inhibition

Answer 32

- _binds at:_ active site - _effect on V_max_: No effect (can be overcome by addition of more substrate) - e_ffect on K_m_: Increased (meaning decreased affinity since there are others competing now)

Question 33

Non-Competitive Inhibitors

Answer 33

- _binds at:_ **allosteric site** (turn enzymes off) - _effect on Vmax:_ **decreases** (some enzymes are turned off thus less product formation) - _effect on Km:_ **Unchanged** (binds at allosteric site, thus doesn't affect substrate binding)

Question 34

Un-competitive Inhibitors

Answer 34

- _binds at:_ allosteric site of ES compelx (after substrate binds) - e_ffect on Vmax:_ decreases (some enzymes inactivated, less product formed) - _effect on Km:_ decreases (greater affinity since the substrate gets locked in)

Question 35

Mixed Inhibitors

Answer 35

- _binds at_: allosteric site of ES compelx (after substrate binds) OR allosteric site on E alone (Δ shape of active site) - _effect on Vmax_: decreases (since mimic uncom or noncom) - _effect on Km_: increased, decreased, or unchanged (need to know more about inhibitor)

Question 36

Describe Key components of Lineweaver-Burk Plots

Answer 36

Inverse Plots: 1/V vs. 1/[S] V = rate of product formation [S] = concentration of substrate y-intercept: 1/Vmax x-intercept: -1/Km As you approach interssection point on the graph, the denominator is getting bigger

Question 37

Type of Inhibitors in these graphs: ![]()

Answer 37

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Question 38

Monomers of Carbohydrates and formula

Answer 38

Carbohydrates C_nH_2nO_n

Question 39

common monosaccharides

Answer 39

_6 Carbon Sugars_ glucose fructose galactose _5 Carbon Sugars_ ribose deoxyribose

Question 40

Most common disaccharides and their constituent components

Answer 40

For the MCAT, they will all be something plus glucose 1) Maltose - glucose + glucose 2) Sucrose - glucose + fructose 3) Lactose = glucose + galactose

Question 41

3 most common and their function

Answer 41

Glycogen: animal glucose storage Starch: plant glucose storage Cellulose: plant structure (humans can't digest)

Question 42

Functions of Carbohydrates

Answer 42

* Energy * cells preferred energy storage * think reduction of glucose via cellular respiration * Cell surface markers * distinguishes b/w different types of cells (liver vs. muscle) * adhesion * carbs are sticky

Question 43

Monomers of lipids

Answer 43

hydrocarbons